INFO 2025-06-26 12:42:59,846 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 12:42:59,846 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled files exist in archive, but not processed by reprocess_surveys.m INFO 2025-06-26 12:42:59,846 process.py process_mission():449 [1] Processing AUVCTD mission 2007.143.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:42:59,846 process.py download_process():165 [1] Download and processing steps for 2007.143.01 INFO 2025-06-26 12:42:59,847 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007143/2007.143.01 INFO 2025-06-26 12:42:59,847 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007143/2007.143.01 to /data/auv_data/dorado/missionlogs/2007.143.01 INFO 2025-06-26 12:43:06,169 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.143.01 INFO 2025-06-26 12:43:06,170 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/ctdDriver.log (21604131 bytes) INFO 2025-06-26 12:43:07,705 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.143.01/ctdDriver.log: [ 6 32 157 250 333 397 666 762 767 845 1005 1017 1157 1198 1543 1603 1618 2025 2175 2565 2859 3045 3242 3279 3831 3841 3891 4427 4616 4841 4932 5251 5341 5350 5429 5685 5728 6670 7239 7822 8035 8095 8193 8563 8565 9621 10019 10380 10976 12323 13777 15241 16217 16537 16666 18163 19577 22559 22939 24289 24873 27064 27840 28584 29135 29329 31854 32833 33107 36780 37646 38999 40617 42758 43098 43631 44024 44197 45961 47771 48124 48416 53778 55624 57648 62643 63128 63246 64184 67856 69756 69961 70629 71419 72452 73714 76679 76873 77047 78133 83392 83985 84795 88577 90109 93137 94892 96828 105330 105713 106919 110260 112056 115644 116978 118972 119565 119836 123122 123146 123697 126679 128881 129611 130646 133515 133793 133911 134114 137127 138149 139331 140907 142371 143845 145789 148901 153151 153452 157273 159376 160211 162248 163172 163990 169082 169362 169379 170706 172670 172802 179369 180163 183155 183592 184138 187007 190705 193331 197566 197817 199360 199811 200477 203505 204284 204933 205660 206375 209345 211000 213160 213272 217715 219161 219327 225235 226535 226825 228163 233206 233386 234676 235668 239018 240063 244577] INFO 2025-06-26 12:43:07,767 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/ctdDriver2.log (21602189 bytes) INFO 2025-06-26 12:43:09,322 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.143.01/ctdDriver2.log: [ 14 139 233 316 380 649 732 745 827 987 999 1139 1180 1468 1524 1584 1599 2006 2156 2546 2840 3026 3223 3260 3812 3872 4408 4597 4822 4913 5233 5323 5332 5411 5583 5667 5710 6652 7221 7804 8017 8077 8175 8545 8547 9603 10001 10362 10958 12094 12306 13760 15225 16201 16521 16650 22543 22922 23513 24272 24856 24966 27823 28567 29118 29312 31837 32816 33090 34165 36763 37629 38982 40601 40997 42743 43083 44181 45944 47754 48107 48399 53762 55609 61509 62629 63115 63234 64171 69744 69949 70616 71406 72438 73700 76858 77032 78119 83378 83971 84781 87261 88565 88566 91088 93124 96815 105317 105700 106907 110249 112045 115631 116965 118960 119552 119823 123108 123683 128867 129597 130632 133005 133502 133780 133899 134101 137115 138138 140895 142359 143834 145778 148890 153139 153440 156840 157263 160199 162236 163978 169070 169349 169367 170693 172657 172788 177408 178759 179356 180150 180661 182097 183143 183579 184125 187713 190690 193316 197551 197802 199345 199797 200462 203491 204038 204269 204919 209328 210983 213142 213254 217697 219144 219309 226518 228145 229284 233189 233369 234323 235649 240042 244554] INFO 2025-06-26 12:43:09,395 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/gps.log (113252 bytes) INFO 2025-06-26 12:43:09,415 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/hydroscatlog.log (14730614 bytes) INFO 2025-06-26 12:43:11,153 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.143.01/hydroscatlog.log: [ 3 28 107 113 232 316 474 603 611 716 743 840 906 1062 1096 1235 1565 1590 1683 1803 2085 2255 2432 2637 2650 2944 3058 3130 3327 3636 3784 3915 3975 4512 4701 5338 5371 5428 5516 5771 5815 6758 7362 8123 8281 8650 8651 9710 10588 11065 12055 12143 12411 12911 13152 13866 15122 15896 18165 18251 18623 19522 20030 20031 22645 23025 23616 24957 25897 26083 27147 27432 27924 28667 29218 29413 29744 32916 33190 33787 36862 37728 39175 41094 41382 42841 43180 43181 47843 47851 48495 49412 49896 53856 55031 55607 55703 56608 56967 62768 63204 64259 65507 67930 69830 70703 70704 71977 72524 76748 76943 84052 84862 85423 88645 91167 91752 91753 93202 94956 97562 103605 105390 105391 105773 106980 108198 109242 110320 110321 111061 111276 112115 113636 115700 117034 119028 119620 119891 123177 123750 128932 129662 130464 130697 133068 133843 134164 134197 137176 137395 139380 140955 142418 143891 145696 145835 148064 153193 157314 159417 162286 163211 164027 168182 169396 170740 172834 175681 177451 177452 179399 180191 180702 183621 187752 190680 190730 193354 197838 199381 199830 203524 204069 204300 204520 204950 205677 209360 211015 213173 213285 219337 226542 229306 231149 233211 234345 234613 234681 239022 240505 243171] INFO 2025-06-26 12:43:11,197 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/navigation.log (72339082 bytes) INFO 2025-06-26 12:43:16,436 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/isuslog.log (1375957 bytes) INFO 2025-06-26 12:43:16,574 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/parosci.log (25820102 bytes) INFO 2025-06-26 12:43:18,810 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/tailCone.log (2980651 bytes) INFO 2025-06-26 12:43:19,196 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.143.01/biolume.log (16708556 bytes) INFO 2025-06-26 12:43:20,891 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:43:21,769 logs2netcdfs.py download_process_logs():807 [1] Time to process: 15.60 seconds WARNING 2025-06-26 12:43:21,770 process.py download_process():196 [1] No lopc.bin file for 2007.143.01 INFO 2025-06-26 12:43:21,770 process.py calibrate():227 [1] Calibration steps for 2007.143.01 INFO 2025-06-26 12:43:22,187 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 12:43:22,190 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:43:22,998 calibrate.py _nudge_pos():1806 [1] 102: 0.110 0.0006525 -0.0004412 2948 9.95 9.750 -8.219 2007-05-23T22:26:47.039941376 INFO 2025-06-26 12:43:23,603 calibrate.py _nudge_pos():1806 [1] 160: 0.100 0.0038539 -0.0007626 10316 34.55 16.585 -4.091 2007-05-23T23:02:17.044026112 INFO 2025-06-26 12:43:24,168 calibrate.py _nudge_pos():1806 [1] 213: 0.110 0.0034586 -0.0011378 10455 34.93 14.725 -6.036 2007-05-23T23:38:05.036878592 INFO 2025-06-26 12:43:24,888 calibrate.py _nudge_pos():1806 [1] 281: 0.110 -0.0003388 -0.0003951 9673 32.28 -1.561 -2.268 2007-05-24T00:11:29.039595008 INFO 2025-06-26 12:43:25,646 calibrate.py _nudge_pos():1806 [1] 353: 0.110 -0.0007245 -0.0004890 16301 54.41 -1.979 -1.665 2007-05-24T01:07:05.041063424 INFO 2025-06-26 12:43:25,680 calibrate.py _nudge_pos():1806 [1] 356: 0.110 0.0000072 0.0000100 50 0.16 6.543 11.341 2007-05-24T01:07:17.040241152 INFO 2025-06-26 12:43:26,492 calibrate.py _nudge_pos():1806 [1] 432: 0.100 -0.0007726 -0.0004874 15901 53.05 -2.164 -1.702 2007-05-24T02:01:35.037053184 INFO 2025-06-26 12:43:27,221 calibrate.py _nudge_pos():1806 [1] 500: 0.090 -0.0006781 -0.0004663 15098 50.38 -1.999 -1.715 2007-05-24T02:53:05.045372928 INFO 2025-06-26 12:43:28,011 calibrate.py _nudge_pos():1806 [1] 573: 0.100 0.0009057 0.0007251 16187 54.00 2.491 2.488 2007-05-24T03:48:17.038486016 INFO 2025-06-26 12:43:28,626 calibrate.py _nudge_pos():1806 [1] 629: 0.100 0.0010476 0.0003952 9826 32.78 4.745 2.234 2007-05-24T04:21:59.039969536 INFO 2025-06-26 12:43:28,638 calibrate.py _nudge_pos():1806 [1] 630: 0.100 -0.0000073 0.0000188 20 0.06 -17.160 54.960 2007-05-24T04:22:03.039695616 INFO 2025-06-26 12:43:29,240 calibrate.py _nudge_pos():1806 [1] 684: 0.100 0.0006436 -0.0001613 5618 18.75 5.097 -1.595 2007-05-24T04:41:41.038996992 INFO 2025-06-26 12:43:30,108 calibrate.py _nudge_pos():1806 [1] 763: 0.100 0.0028412 0.0008100 10519 35.10 12.015 4.277 2007-05-24T05:18:05.039382784 INFO 2025-06-26 12:43:30,153 calibrate.py _nudge_pos():1806 [1] 767: 0.100 0.0000126 -0.0000117 95 0.31 5.986 -6.914 2007-05-24T05:18:27.037875712 INFO 2025-06-26 12:43:30,825 calibrate.py _nudge_pos():1806 [1] 828: 0.100 0.0008675 0.0012149 8462 28.23 4.560 7.974 2007-05-24T05:47:41.037718528 INFO 2025-06-26 12:43:31,381 calibrate.py _nudge_pos():1806 [1] 878: 0.090 0.0009683 0.0012745 13779 45.98 3.124 5.136 2007-05-24T06:34:29.045356800 INFO 2025-06-26 12:43:31,959 calibrate.py _nudge_pos():1806 [1] 931: 0.090 -0.0008300 0.0019117 14671 48.93 -2.515 7.240 2007-05-24T07:24:17.040664832 INFO 2025-06-26 12:43:32,583 calibrate.py _nudge_pos():1806 [1] 987: 0.090 -0.0002022 0.0003942 14319 47.78 -0.627 1.529 2007-05-24T08:12:59.040494080 INFO 2025-06-26 12:43:33,264 calibrate.py _nudge_pos():1806 [1] 1047: 0.090 0.0000184 0.0000012 13919 46.41 0.059 0.005 2007-05-24T09:00:23.035667456 INFO 2025-06-26 12:43:33,849 calibrate.py _nudge_pos():1806 [1] 1100: 0.090 -0.0000663 -0.0000419 10110 33.73 -0.291 -0.230 2007-05-24T09:34:59.043451136 INFO 2025-06-26 12:43:34,452 calibrate.py _nudge_pos():1806 [1] 1153: 0.090 0.0000168 -0.0000082 3549 11.83 0.210 -0.128 2007-05-24T09:47:41.041250816 INFO 2025-06-26 12:43:35,038 calibrate.py _nudge_pos():1806 [1] 1207: 0.090 0.0001431 -0.0005064 8099 27.01 0.785 -3.473 2007-05-24T10:15:35.036574208 INFO 2025-06-26 12:43:35,683 calibrate.py _nudge_pos():1806 [1] 1267: 0.090 0.0003190 -0.0004365 8338 27.81 1.699 -2.908 2007-05-24T10:44:23.038197760 INFO 2025-06-26 12:43:36,282 calibrate.py _nudge_pos():1806 [1] 1322: 0.080 0.0009699 0.0016199 17536 58.50 2.457 5.131 2007-05-24T11:43:47.044046592 INFO 2025-06-26 12:43:36,358 calibrate.py _nudge_pos():1806 [1] 1329: 0.090 -0.0000236 -0.0000075 120 0.40 -8.808 -3.512 2007-05-24T11:44:17.041991680 INFO 2025-06-26 12:43:36,861 calibrate.py _nudge_pos():1806 [1] 1376: 0.090 0.0019968 0.0019025 16045 53.53 5.528 6.586 2007-05-24T12:38:35.038803456 INFO 2025-06-26 12:43:37,424 calibrate.py _nudge_pos():1806 [1] 1428: 0.090 0.0041487 0.0025432 21753 72.55 8.478 6.496 2007-05-24T13:51:59.037109248 INFO 2025-06-26 12:43:38,087 calibrate.py _nudge_pos():1806 [1] 1488: 0.080 0.0033132 0.0021095 18381 61.31 8.014 6.375 2007-05-24T14:54:17.041038336 INFO 2025-06-26 12:43:38,632 calibrate.py _nudge_pos():1806 [1] 1538: 0.080 0.0017458 0.0006178 6950 23.18 11.171 4.939 2007-05-24T15:18:17.042391552 INFO 2025-06-26 12:43:38,877 calibrate.py _nudge_pos():1862 [1] 1527: - - - 3 0.01 - - INFO 2025-06-26 12:43:38,877 calibrate.py _nudge_pos():1868 [1] Points in final series = 306511 WARNING 2025-06-26 12:43:39,366 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 12:44:10,062 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 7 of 245292 INFO 2025-06-26 12:44:11,910 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:44:29,410 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 21 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:44:31,223 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 21 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:44:31,227 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.143.01/ctd1.nc INFO 2025-06-26 12:44:31,229 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:44:31,229 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 12:44:31,229 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:44:44,682 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:44:46,509 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:44:46,513 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.143.01/ctd2.nc INFO 2025-06-26 12:44:46,514 calibrate.py _range_qc_combined_nc():898 [1] Setting 175 ctd2_salinity values to NaN INFO 2025-06-26 12:44:46,515 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 12:44:46,515 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:44:46,598 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:44:49,403 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3610222 3610223 3610224] INFO 2025-06-26 12:44:49,931 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:44:49,938 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 12:44:49,938 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.143.01 ERROR 2025-06-26 12:44:49,938 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.143.01 INFO 2025-06-26 12:44:49,989 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_cal.nc INFO 2025-06-26 12:45:09,084 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 12:45:09,089 process.py align():251 [1] Alignment steps for 2007.143.01 INFO 2025-06-26 12:45:09,127 align.py process_cal():139 [1] Processing dorado_2007.143.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.143.01 INFO 2025-06-26 12:45:09,206 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:45:09,214 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:45:09,405 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:45:09,416 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:45:09,606 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:45:09,617 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:45:09,735 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:45:09,735 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:45:09,809 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:45:09,819 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:45:10,006 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:10,016 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:45:10,176 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:10,185 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:45:10,346 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:10,355 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:45:10,517 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:10,526 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:10,693 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:10,702 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:10,865 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:10,873 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:11,042 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:11,051 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:11,212 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:11,221 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:11,384 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:11,393 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:11,554 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:11,565 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:11,728 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:11,737 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:11,900 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:11,909 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:12,072 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:12,080 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:12,244 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:12,253 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:12,416 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:12,426 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:12,587 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:12,598 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:12,760 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:12,769 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:12,931 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:12,940 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:13,104 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:13,113 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:13,275 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.143.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:45:13,283 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:45:13,478 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:45:13,600 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:45:13,722 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:45:13,850 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:45:13,981 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 12:45:14,020 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_align.nc INFO 2025-06-26 12:45:14,152 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 12:45:14,154 process.py resample():273 [1] Resampling steps for 2007.143.01 INFO 2025-06-26 12:45:14,155 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:45:14,186 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_align.nc mission netCDF file INFO 2025-06-26 12:45:14,193 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_align.nc mission netCDF file INFO 2025-06-26 12:45:14,195 resample.py get_mission_start_end():1145 [1] navigation: 2007-05-23T22:15:43.365406208 to 2007-05-24T15:18:39.640843264 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 12:45:14,198 resample.py get_mission_start_end():1145 [1] hs2 : 2007-05-23T22:15:17.147202304 to 2007-05-24T15:18:39.680840448 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:45:14,200 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-05-23T22:15:35.635935744 to 2007-05-24T15:18:39.560848640 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 12:45:14,203 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-05-23T22:15:39.885644800 to 2007-05-24T15:18:39.610845440 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 12:45:14,204 resample.py get_mission_start_end():1145 [1] isus : 2007-05-23T22:16:25.082548480 to 2007-05-24T15:18:38.650910976 (0 days 00:00:01.029929472 before mission_end) INFO 2025-06-26 12:45:14,206 resample.py get_mission_start_end():1145 [1] biolume : 2007-05-23T22:15:09.207712000 to 2007-05-24T15:18:39.080847616 (0 days 00:00:00.599992832 before mission_end) INFO 2025-06-26 12:45:14,207 resample.py get_mission_start_end():1145 [1] tailcone : 2007-05-23T22:15:14.837360640 to 2007-05-24T15:18:38.900893952 (0 days 00:00:00.779946496 before mission_end) INFO 2025-06-26 12:45:14,208 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_align.nc mission netCDF file INFO 2025-06-26 12:45:14,209 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:14,829 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:14,928 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,026 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,122 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,203 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,285 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,366 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,447 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,524 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,601 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,678 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,756 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,832 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,909 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:15,986 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,062 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,141 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,223 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,307 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,386 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,466 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,545 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,575 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,600 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,625 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,654 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:16,685 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:45:17,120 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_1S.nc INFO 2025-06-26 12:45:30,409 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.143.01/dorado_2007.143.01_1S_Gulper.txt INFO 2025-06-26 12:45:30,409 process.py archive():337 [1] Archiving steps for 2007.143.01 INFO 2025-06-26 12:45:30,409 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01, BASE_PATH = /data/auv_data INFO 2025-06-26 12:45:30,411 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:45:30,412 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.143.01_1S.nc INFO 2025-06-26 12:45:30,459 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:45:30,460 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.143.01_cal.nc INFO 2025-06-26 12:45:30,678 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:45:30,679 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.143.01_align.nc INFO 2025-06-26 12:45:30,878 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:45:30,941 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:30,998 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,003 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,045 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,235 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,244 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,312 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,329 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,485 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007143/2007.143.01 done. INFO 2025-06-26 12:45:31,486 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:45:31,487 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.143.01_1S_Gulper.txt INFO 2025-06-26 12:45:31,492 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.143.01/dorado_2007.143.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 12:45:31,492 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.143.01/dorado_2007.143.01_processing.log /Volumes/AUVCTD/surveys/2007/netcdf